Ok.
Well my water is green, it has been that way all summer. I'm assuming the algae in there will die with the cold temperatures making the water clearer(assuming my water clarity problem is due to algae), is this true? Is there a chance the algae won't die? I imagine the bacteria I put in there will die but I've seen there are some strains that can live in colder conditions, unfortunately I don't know what strains I have. I'm trying to decide when to pull the plug on my aerator.
What's the coldest temperature I could hold out to?
Yeah, most of the phytoplankton that is alive in the warmer water will die, but enough will be alive to repopulate the pond next year.
As for temp, how thick is your winter coat, and do you have good boots and gloves?

Water temps in the 40's-50's would be fine, although I think running it in the winter is even more important than the summer up here where we can get heavy snow cover on the pond.